Software Packages for Detecting HRD Scores in Tumor-Only Cancer Samples

can you tell me or suggest some software packages or pipelines for detect hrd scores in tumor only (without matched normal) samples in cancer?

Detecting homologous recombination deficiency (HRD) scores in tumor-only samples (without matched normal) can be challenging, but there are several software packages and pipelines that have been developed to address this. Here are some options you might consider:

1. HRDetect:

   • Description: HRDetect is a machine learning-based tool that integrates multiple types of genomic data to predict HRD status.
   • Input: Whole-genome sequencing (WGS) data.
   • Link: HRDetect GitHub

2. ScarHRD:

   • Description: ScarHRD is a tool that quantifies HRD based on the presence of specific genomic scars, such as loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST).
   • Input: Copy number variation (CNV) data from WGS or whole-exome sequencing (WES).
   • Link: ScarHRD GitHub

3. CHORD:

   • Description: CHORD is a classifier that uses mutational signatures to predict HRD status. It can work with both WGS and WES data.
   • Input: Somatic mutation data.
   • Link: CHORD GitHub

4. SigMA:

   • Description: SigMA (Signature Mutational Analysis) is a tool that can identify mutational signatures associated with HRD from WES data.
   • Input: Somatic mutation data.
   • Link: SigMA GitHub

5. LOHHLA:

   • Description: LOHHLA (Loss Of Heterozygosity in Human Leukocyte Antigen) is a tool that can be used to detect LOH events, which are indicative of HRD.
   • Input: WES or targeted sequencing data.
   • Link: LOHHLA GitHub

6. FACETS:

   • Description: FACETS (Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing) is a tool for allele-specific copy number analysis, which can be used to infer HRD.
   • Input: WES or targeted sequencing data.
   • Link: FACETS GitHub

7. Battenberg:

   • Description: Battenberg is a tool for allele-specific copy number analysis and can be used to detect LOH and other genomic alterations indicative of HRD.
   • Input: WGS data.
   • Link: Battenberg GitHub

8. HRDscore:

   • Description: HRDscore is a tool that calculates an HRD score based on the presence of LOH, TAI, and LST.
   • Input: CNV data from WGS or WES.
   • Link: HRDscore GitHub

When using these tools, it's important to carefully read the documentation and understand the input requirements and limitations. Additionally, some tools may